BCS1 COI pipeline

These scripts are built to run on a server with SLURM.

Script run order

BFC.sh
(trunc.sh)
usearch.sh
mothur_trim.sh
mothur_merge.sh <-> merge_split.sh
MACSE_align.sh <-> mACSE_align_split.sh
mACSE_export.sh
mothur_remove_ref.sh
update_names.sh
precluster.sh
CROP.sh
blast_all.sh
sap_all.sh

BFC.sh

Run BFC to denoise.

eestats2.sh

Use this to check the read quality by basepair.

trunc.sh

Use this to truncate reads if the ends are low quality.

usearch.sh

Be sure to adjust the parameters with in usearch.sh to accomodate the barcode being used.

mothur_trim.sh

merge_split.sh

mACSE_align_split.sh

mothur_remove_ref.sh

Remove sequences from BIOCODE2014_MACSE_313_headers.accnos.

update_names.sh

Removes sequence labels that are no longer in the aligned FASTA file. This step preps for removal in MOTHUR.

precluster.sh

Runs count.seqs, pre.cluster, chimera.uchime, remove.seqs (remove chimeras) commands in MOTHUR.

CROP.sh

Cluster sequences